1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Qin, X.R.
Hayashi, F.
Yokoyama, S.
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
To be Published
0353
Solution structure of the PKD domain from KIAA 1837 protein
10.2210/pdb2yrl/pdb
pdb_00002yrl
10585.358
KIAA1837 protein
PKD domain
1
man
polymer
no
no
GSSGSSGQADAGPDKELTLPVDSTTLDGSKSSDDQKIISYLWEKTQGPDGVQLENANSSVATVTGLQVGTYVFTLTVKDE
RNLQSQSSVNVIVKEESGPSSG
GSSGSSGQADAGPDKELTLPVDSTTLDGSKSSDDQKIISYLWEKTQGPDGVQLENANSSVATVTGLQVGTYVFTLTVKDE
RNLQSQSSVNVIVKEESGPSSG
A
hsk002301805.1
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
sample
cell-free protein synthesis
KIAA1837
9606
Homo sapiens
plasmid
P051025-02
RIKEN Structural Genomics/Proteomics Initiative
RSGI
NPPSFA, National Project on Protein Structural and Functional Analyses
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2007-10-02
1
1
2011-07-13
1
2
2022-03-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
Y
PDBJ
Y
PDBJ
2007-04-02
REL
REL
spectrometer_id 1 for 3D_15N_separated_NOESY; spectrometer_id 2 for 3D_13C_separated_NOESY
structures with the least restraint violations, structures with the lowest energy, target function
100
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
120mM
7.0
ambient
298
K
torsion angle dynamics
1
lowest energy
1.13mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
90% H2O/10% D2O
Varian
collection
VNMR
6.1C
Delaglio, F.
processing
NMRPipe
20030801
Johnson, B.A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.9820
Guntert, P.
structure solution
CYANA
2.0.17
Guntert, P.
refinement
CYANA
2.0.17
800
Varian
INOVA
900
Varian
INOVA
GLY
1
n
1
GLY
1
A
SER
2
n
2
SER
2
A
SER
3
n
3
SER
3
A
GLY
4
n
4
GLY
4
A
SER
5
n
5
SER
5
A
SER
6
n
6
SER
6
A
GLY
7
n
7
GLY
7
A
GLN
8
n
8
GLN
8
A
ALA
9
n
9
ALA
9
A
ASP
10
n
10
ASP
10
A
ALA
11
n
11
ALA
11
A
GLY
12
n
12
GLY
12
A
PRO
13
n
13
PRO
13
A
ASP
14
n
14
ASP
14
A
LYS
15
n
15
LYS
15
A
GLU
16
n
16
GLU
16
A
LEU
17
n
17
LEU
17
A
THR
18
n
18
THR
18
A
LEU
19
n
19
LEU
19
A
PRO
20
n
20
PRO
20
A
VAL
21
n
21
VAL
21
A
ASP
22
n
22
ASP
22
A
SER
23
n
23
SER
23
A
THR
24
n
24
THR
24
A
THR
25
n
25
THR
25
A
LEU
26
n
26
LEU
26
A
ASP
27
n
27
ASP
27
A
GLY
28
n
28
GLY
28
A
SER
29
n
29
SER
29
A
LYS
30
n
30
LYS
30
A
SER
31
n
31
SER
31
A
SER
32
n
32
SER
32
A
ASP
33
n
33
ASP
33
A
ASP
34
n
34
ASP
34
A
GLN
35
n
35
GLN
35
A
LYS
36
n
36
LYS
36
A
ILE
37
n
37
ILE
37
A
ILE
38
n
38
ILE
38
A
SER
39
n
39
SER
39
A
TYR
40
n
40
TYR
40
A
LEU
41
n
41
LEU
41
A
TRP
42
n
42
TRP
42
A
GLU
43
n
43
GLU
43
A
LYS
44
n
44
LYS
44
A
THR
45
n
45
THR
45
A
GLN
46
n
46
GLN
46
A
GLY
47
n
47
GLY
47
A
PRO
48
n
48
PRO
48
A
ASP
49
n
49
ASP
49
A
GLY
50
n
50
GLY
50
A
VAL
51
n
51
VAL
51
A
GLN
52
n
52
GLN
52
A
LEU
53
n
53
LEU
53
A
GLU
54
n
54
GLU
54
A
ASN
55
n
55
ASN
55
A
ALA
56
n
56
ALA
56
A
ASN
57
n
57
ASN
57
A
SER
58
n
58
SER
58
A
SER
59
n
59
SER
59
A
VAL
60
n
60
VAL
60
A
ALA
61
n
61
ALA
61
A
THR
62
n
62
THR
62
A
VAL
63
n
63
VAL
63
A
THR
64
n
64
THR
64
A
GLY
65
n
65
GLY
65
A
LEU
66
n
66
LEU
66
A
GLN
67
n
67
GLN
67
A
VAL
68
n
68
VAL
68
A
GLY
69
n
69
GLY
69
A
THR
70
n
70
THR
70
A
TYR
71
n
71
TYR
71
A
VAL
72
n
72
VAL
72
A
PHE
73
n
73
PHE
73
A
THR
74
n
74
THR
74
A
LEU
75
n
75
LEU
75
A
THR
76
n
76
THR
76
A
VAL
77
n
77
VAL
77
A
LYS
78
n
78
LYS
78
A
ASP
79
n
79
ASP
79
A
GLU
80
n
80
GLU
80
A
ARG
81
n
81
ARG
81
A
ASN
82
n
82
ASN
82
A
LEU
83
n
83
LEU
83
A
GLN
84
n
84
GLN
84
A
SER
85
n
85
SER
85
A
GLN
86
n
86
GLN
86
A
SER
87
n
87
SER
87
A
SER
88
n
88
SER
88
A
VAL
89
n
89
VAL
89
A
ASN
90
n
90
ASN
90
A
VAL
91
n
91
VAL
91
A
ILE
92
n
92
ILE
92
A
VAL
93
n
93
VAL
93
A
LYS
94
n
94
LYS
94
A
GLU
95
n
95
GLU
95
A
GLU
96
n
96
GLU
96
A
SER
97
n
97
SER
97
A
GLY
98
n
98
GLY
98
A
PRO
99
n
99
PRO
99
A
SER
100
n
100
SER
100
A
SER
101
n
101
SER
101
A
GLY
102
n
102
GLY
102
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
LEU
17
A
N
LEU
17
A
O
LYS
94
A
O
LYS
94
A
O
SER
87
A
O
SER
87
A
N
LEU
75
A
N
LEU
75
A
O
VAL
72
A
O
VAL
72
A
N
THR
45
A
N
THR
45
A
N
LEU
26
A
N
LEU
26
A
O
ALA
61
A
O
ALA
61
A
O
THR
64
A
O
THR
64
A
N
GLN
52
A
N
GLN
52
1
A
ALA
11
-85.66
33.69
1
A
PRO
13
-69.74
-175.66
1
A
LEU
19
-38.37
158.62
1
A
VAL
21
-53.21
88.44
1
A
ASP
22
-104.69
43.79
1
A
LYS
30
-93.02
55.58
1
A
VAL
51
-42.76
156.51
1
A
ASN
57
-87.24
34.08
1
A
VAL
68
-55.00
94.87
1
A
ARG
81
-89.74
32.33
1
A
ASN
82
39.17
35.73
1
A
SER
97
-39.38
146.36
2
A
SER
2
-57.56
107.26
2
A
SER
5
-61.33
96.45
2
A
ALA
11
-88.02
31.61
2
A
PRO
13
-69.71
-178.54
2
A
LEU
19
-44.88
158.33
2
A
VAL
51
-45.35
167.91
2
A
ASN
57
-87.75
31.89
2
A
VAL
68
-48.49
101.55
3
A
GLN
8
-124.21
-65.70
3
A
LEU
19
-39.18
159.10
3
A
VAL
21
-49.94
93.44
3
A
ASP
22
-107.99
40.59
3
A
LYS
30
-107.66
45.72
3
A
SER
31
-54.82
-175.07
3
A
ASP
34
34.61
35.54
3
A
VAL
68
-42.19
109.74
3
A
SER
100
-67.84
82.94
4
A
GLN
8
-106.87
43.05
4
A
LEU
19
-38.18
158.32
4
A
VAL
21
-51.20
99.14
4
A
LYS
30
-39.96
-25.42
4
A
VAL
51
-41.73
160.97
4
A
ASN
57
-87.18
35.13
4
A
ARG
81
-88.32
31.18
4
A
GLU
96
-49.77
100.99
5
A
ASP
14
-36.83
138.13
5
A
LEU
19
-40.64
159.12
5
A
VAL
21
-49.51
87.75
5
A
ASP
22
-105.08
44.01
5
A
VAL
51
-48.08
164.20
5
A
VAL
68
-37.95
99.60
5
A
ASN
82
45.78
25.84
6
A
ALA
11
-37.58
-35.27
6
A
LEU
19
-44.65
158.22
6
A
VAL
21
-50.05
93.18
6
A
SER
29
-38.17
-34.41
6
A
GLN
35
-101.21
43.30
6
A
ASN
57
-87.07
34.27
6
A
VAL
68
-53.63
95.38
6
A
GLU
96
-52.09
177.11
6
A
SER
97
-38.95
117.16
7
A
ASP
14
-39.11
150.37
7
A
LEU
19
-38.72
157.46
7
A
VAL
21
-50.29
92.41
7
A
LYS
30
-76.78
47.76
7
A
SER
31
-94.69
49.23
7
A
VAL
51
-44.55
158.78
7
A
VAL
68
-34.20
120.23
7
A
ASN
82
41.67
29.95
7
A
SER
97
-117.08
78.04
8
A
ASP
14
-39.45
149.60
8
A
LEU
19
-37.74
156.23
8
A
VAL
21
-56.87
86.75
8
A
SER
32
-36.48
130.18
8
A
VAL
51
-44.41
166.15
8
A
SER
59
-37.97
-29.21
8
A
VAL
68
-39.00
111.92
8
A
ASN
82
44.34
27.01
8
A
SER
101
-124.70
-50.48
9
A
ALA
11
-99.52
33.56
9
A
PRO
13
-69.76
-178.21
9
A
LEU
19
-39.16
156.18
9
A
VAL
21
-55.62
90.40
9
A
SER
29
-76.11
48.76
9
A
SER
32
-36.11
108.39
9
A
VAL
68
-43.98
107.36
10
A
LEU
19
-44.72
157.93
10
A
VAL
21
-47.35
97.74
10
A
LYS
30
-91.87
47.45
10
A
GLN
35
-58.20
171.85
10
A
VAL
68
-43.91
100.85
10
A
GLN
86
-171.27
144.92
10
A
PRO
99
-69.85
88.65
10
A
SER
101
-93.13
-61.13
11
A
SER
2
-169.09
116.99
11
A
ALA
11
-86.77
41.09
11
A
LEU
19
-38.94
156.02
11
A
VAL
21
-52.13
102.38
11
A
ASN
57
-84.56
32.10
11
A
VAL
68
-39.17
105.61
11
A
ASN
82
43.84
28.59
11
A
SER
101
-36.97
130.46
12
A
ALA
11
-36.99
-34.30
12
A
LEU
19
-42.40
158.47
12
A
VAL
21
-49.84
91.05
12
A
ASP
22
-108.05
43.03
12
A
LYS
30
-80.39
48.76
12
A
SER
31
-96.34
44.31
12
A
SER
32
-174.90
146.26
12
A
VAL
68
-43.81
99.62
12
A
SER
87
-161.99
116.60
12
A
GLU
96
-39.41
148.76
12
A
SER
100
-121.96
-55.80
13
A
GLN
8
-97.50
50.40
13
A
ALA
9
-171.25
118.32
13
A
ALA
11
-98.62
35.62
13
A
PRO
13
-69.71
-174.08
13
A
LEU
19
-40.79
159.14
13
A
VAL
21
-54.34
95.90
13
A
LYS
30
-83.45
47.13
13
A
ASP
34
-39.88
158.59
13
A
VAL
51
-46.29
169.69
13
A
VAL
68
-37.45
103.76
13
A
SER
101
-172.60
116.58
14
A
PRO
13
-69.81
-174.92
14
A
LEU
19
-37.96
155.79
14
A
VAL
21
-58.87
82.50
14
A
ASP
33
-60.79
91.92
14
A
VAL
51
-41.21
163.33
14
A
SER
59
-37.92
-31.75
14
A
VAL
68
-37.34
94.57
14
A
ARG
81
-84.95
32.75
14
A
ASN
82
40.07
27.52
14
A
GLU
96
-42.03
155.09
15
A
SER
5
-50.13
95.15
15
A
ASP
10
-34.52
104.28
15
A
ASP
14
-37.64
138.37
15
A
LEU
19
-40.09
158.10
15
A
VAL
21
-47.27
91.86
15
A
LYS
30
-82.66
48.98
15
A
SER
32
-35.17
149.03
15
A
VAL
51
-47.61
165.18
15
A
VAL
68
-41.79
109.61
15
A
SER
97
-59.08
108.51
16
A
SER
2
-41.20
151.63
16
A
ALA
9
-34.14
144.35
16
A
LEU
19
-45.06
156.16
16
A
VAL
21
-46.97
96.38
16
A
LYS
30
-91.35
34.20
16
A
SER
32
-174.34
144.52
16
A
ASN
57
-84.31
31.86
16
A
VAL
68
-35.39
94.87
16
A
PRO
99
-69.81
-178.31
16
A
SER
100
-125.70
-54.11
17
A
PRO
13
-69.78
-177.11
17
A
LEU
19
-41.92
155.64
17
A
VAL
21
-50.54
98.92
17
A
LYS
30
-98.77
40.77
17
A
GLN
35
-98.99
59.32
17
A
ILE
38
-90.82
32.43
17
A
VAL
51
-45.14
164.32
17
A
VAL
68
-47.84
90.36
17
A
PRO
99
-69.72
87.47
18
A
SER
3
36.13
41.83
18
A
ASP
10
-119.73
69.79
18
A
LEU
19
-38.99
156.01
18
A
VAL
21
-53.42
92.10
18
A
SER
29
-94.17
42.46
18
A
SER
32
-38.55
144.34
18
A
GLN
35
-101.64
70.23
18
A
ASN
57
-86.25
35.84
18
A
VAL
68
-39.10
96.15
18
A
ARG
81
-85.40
32.38
18
A
ASN
82
39.08
34.79
18
A
SER
85
-161.73
119.44
18
A
SER
101
-59.82
105.43
19
A
GLN
8
-85.37
45.52
19
A
ASP
10
-119.88
78.75
19
A
LEU
19
-42.89
155.85
19
A
VAL
21
-48.47
93.03
19
A
SER
31
-35.97
150.44
19
A
SER
32
-38.31
119.55
19
A
LYS
36
-34.86
147.49
19
A
ASN
55
44.97
26.74
19
A
ASN
57
-90.28
31.10
19
A
VAL
68
-35.89
94.78
19
A
SER
100
-107.90
-61.78
20
A
LEU
19
-41.46
159.25
20
A
VAL
21
-49.47
94.89
20
A
LYS
30
-92.72
48.88
20
A
LYS
36
-36.57
123.04
20
A
ASN
57
-88.68
30.17
20
A
ARG
81
-92.57
32.16
20
A
ASN
82
45.01
25.83
20
A
SER
101
-59.37
88.06
Solution structure of the PKD domain from KIAA 1837 protein
1
N
N
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
PKD domain, KIAA1837 protein, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, STRUCTURAL GENOMICS, UNKNOWN FUNCTION
A
LEU
19
A
LEU
19
1
A
PRO
20
A
PRO
20
-0.16
A
LEU
19
A
LEU
19
2
A
PRO
20
A
PRO
20
-0.10
A
LEU
19
A
LEU
19
3
A
PRO
20
A
PRO
20
-0.16
A
LEU
19
A
LEU
19
4
A
PRO
20
A
PRO
20
-0.12
A
LEU
19
A
LEU
19
5
A
PRO
20
A
PRO
20
-0.15
A
LEU
19
A
LEU
19
6
A
PRO
20
A
PRO
20
-0.08
A
LEU
19
A
LEU
19
7
A
PRO
20
A
PRO
20
-0.08
A
LEU
19
A
LEU
19
8
A
PRO
20
A
PRO
20
-0.07
A
LEU
19
A
LEU
19
9
A
PRO
20
A
PRO
20
-0.13
A
LEU
19
A
LEU
19
10
A
PRO
20
A
PRO
20
-0.20
A
LEU
19
A
LEU
19
11
A
PRO
20
A
PRO
20
-0.17
A
LEU
19
A
LEU
19
12
A
PRO
20
A
PRO
20
-0.21
A
LEU
19
A
LEU
19
13
A
PRO
20
A
PRO
20
-0.11
A
LEU
19
A
LEU
19
14
A
PRO
20
A
PRO
20
-0.11
A
LEU
19
A
LEU
19
15
A
PRO
20
A
PRO
20
-0.11
A
LEU
19
A
LEU
19
16
A
PRO
20
A
PRO
20
-0.13
A
LEU
19
A
LEU
19
17
A
PRO
20
A
PRO
20
-0.17
A
LEU
19
A
LEU
19
18
A
PRO
20
A
PRO
20
-0.11
A
LEU
19
A
LEU
19
19
A
PRO
20
A
PRO
20
-0.16
A
LEU
19
A
LEU
19
20
A
PRO
20
A
PRO
20
-0.17
Q96JJ0_HUMAN
UNP
1
243
Q96JJ0
QADAGPDKELTLPVDSTTLDGSKSSDDQKIISYLWEKTQGPDGVQLENANSSVATVTGLQVGTYVFTLTVKDERNLQSQS
SVNVIVKEE
243
331
2YRL
8
96
Q96JJ0
A
1
8
96
1
expression tag
GLY
1
2YRL
A
Q96JJ0
UNP
1
1
expression tag
SER
2
2YRL
A
Q96JJ0
UNP
2
1
expression tag
SER
3
2YRL
A
Q96JJ0
UNP
3
1
expression tag
GLY
4
2YRL
A
Q96JJ0
UNP
4
1
expression tag
SER
5
2YRL
A
Q96JJ0
UNP
5
1
expression tag
SER
6
2YRL
A
Q96JJ0
UNP
6
1
expression tag
GLY
7
2YRL
A
Q96JJ0
UNP
7
1
expression tag
SER
97
2YRL
A
Q96JJ0
UNP
97
1
expression tag
GLY
98
2YRL
A
Q96JJ0
UNP
98
1
expression tag
PRO
99
2YRL
A
Q96JJ0
UNP
99
1
expression tag
SER
100
2YRL
A
Q96JJ0
UNP
100
1
expression tag
SER
101
2YRL
A
Q96JJ0
UNP
101
1
expression tag
GLY
102
2YRL
A
Q96JJ0
UNP
102
4
3
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
15
A
LYS
15
A
THR
18
A
THR
18
A
GLN
84
A
GLN
84
A
LYS
94
A
LYS
94
A
THR
70
A
THR
70
A
LYS
78
A
LYS
78
A
TRP
42
A
TRP
42
A
GLN
46
A
GLN
46
A
SER
23
A
SER
23
A
ASP
27
A
ASP
27
A
VAL
60
A
VAL
60
A
THR
64
A
THR
64
A
GLN
52
A
GLN
52
A
GLU
54
A
GLU
54